对 18421 条系的基因组研究揭示了水稻的遗传结构。

Genomic investigation of 18,421 lines reveals the genetic architecture of rice.

机构信息

Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China.

State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China.

出版信息

Science. 2024 Jul 5;385(6704):eadm8762. doi: 10.1126/science.adm8762.

DOI:10.1126/science.adm8762

PMID:38963845

Abstract

Understanding how numerous quantitative trait loci (QTL) shape phenotypic variation is an important question in genetics. To address this, we established a permanent population of 18,421 (18K) rice lines with reduced population structure. We generated reference-level genome assemblies of the founders and genotyped all 18K-rice lines through whole-genome sequencing. Through high-resolution mapping, 96 high-quality candidate genes contributing to variation in 16 traits were identified, including and verified as causal genes for panicle number and heading date, respectively. We identified epistatic QTL pairs and constructed a genetic interaction network with 19 genes serving as hubs. Overall, 170 masking epistasis pairs were characterized, serving as an important factor contributing to genetic background effects across diverse varieties. The work provides a basis to guide grain yield and quality improvements in rice.

摘要

了解众多数量性状位点（QTL）如何塑造表型变异是遗传学中的一个重要问题。为了解决这个问题，我们建立了一个由 18421 条（18K）水稻品系组成的永久性群体，其群体结构得到了降低。我们对创始人进行了参考水平的基因组组装，并通过全基因组测序对所有 18K-水稻品系进行了基因型分析。通过高分辨率作图，鉴定出了 96 个高质量的候选基因，这些基因分别与 16 个性状的变异有关，其中和分别被验证为穗数和抽穗期的因果基因。我们鉴定了上位性 QTL 对，并构建了一个包含 19 个基因作为枢纽的遗传相互作用网络。总的来说，我们描述了 170 个掩蔽上位性对，它们是不同品种中遗传背景效应的一个重要因素。这项工作为指导水稻的产量和品质改良提供了基础。